OMA


25399418	The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. [PMID: 25399418] Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. Abstract The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2015:43(Database issue) \| 132 Citations (from Europe PMC, 2025-03-22)
21113020	OMA 2011: orthology inference among 1000 complete genomes. [PMID: 21113020] Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. Abstract OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline--in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org. Nucleic Acids Res. 2011:39(Database issue) \| 138 Citations (from Europe PMC, 2025-03-22)

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. [PMID: 25399418]

Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C.

Abstract

The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 132 Citations (from Europe PMC, 2025-03-22)

OMA 2011: orthology inference among 1000 complete genomes. [PMID: 21113020]

Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C.

Abstract

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline--in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org.

Nucleic Acids Res. 2011:39(Database issue) | 138 Citations (from Europe PMC, 2025-03-22)

URL:	http://omabrowser.org/oma/home/
Full name:	The Orthologous Matrix project
Description:	The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes
Year founded:	2011
Last update:	2015-04-03
Version:	v1.0.2
Accessibility:	Accessible
Country/Region:	United Kingdom

Data type:	DNA Protein
Data object:	Archaea Bacteria Fungi
Database category:	Phylogeny and homology
Major species:	NA
Keywords:	orthologous matrix

University/Institution:	University College London
Address:	Gower Street,London WC1E 6BT,UK
City:	London
Province/State:
Country/Region:	United Kingdom
Contact name (PI/Team):	Christophe Dessimoz
Contact email (PI/Helpdesk):	c.dessimoz@ucl.ac.uk

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Database Commons a catalog of worldwide biological databases